How to find and replace multiple words and matching them with perl

Hi to all PERL programmers,
I have data like this
DATA HAVE
pop A B C D E

P1 T/T C/C C/C T/T C/C
P2 A/A G/G C/C T/T C/C
1 A/A G/G C/C T/T C/C
2 A/A G/G C/C T/T C/C
3 A/T A/C A/G A/T A/C
4 T/A T/G T/C T/A T/G
5 G/A G/T G/C G/A G/T
6 C/A C/T C/G C/A C/T
1.first I want to convert all A/A to A, T/T to T, C/C to C, G/G to G, Z/Z to - and -/- to -
2. Now I want to know status from A to E by comparing P1 with P2, if P1=P2 then status from A to E is mono or any one of P1 or P2 contains Z/Z or -/- then status from A to E is mono else status from A to E is poly
3. I want to match 1 in pop column with p2 in pop column for A to E
4. if 1 in pop column matches to p2 in pop column and its status is poly only then I would like to give 1 other wise as such, if it is mono I do not want to do anything.
5. Now I will calculate # 1's and # H's
6. finally I will calculate %sim with this formula =((#1*2+#H)/((#1+#H)*2))*100.

Now i donot have any idea on how to proceed for next steps can any one help me to solve this problem?
any help would be highly appreciated. I want to attach my sample data here but i do not know how to attach file here and sorry for that.
Thanks in Advance
Regards.